The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Bone Marrow Procedures in Children Welfare Teaching Hospital/Medical City Complex Indications and results

Background: Bone marrow aspiration (BMA) and biopsy is a procedure that is used to evaluate the cause of abnormal blood test results, to confirm a diagnosis or check the status of severe anemia of unknown cause, to evaluate abnormalities in the blood's ability to store iron and also to diagnose infection. Objectives: To identify the main indications of bone marrow aspiration and the most common diagnoses encountered in children welfare teaching hospital. Patients and methods: This was a prospective and retrospective descriptive study over 6- month period from 8th of February 2010 to 8th of August 2010 in children younger than 14 years. All bone marrow aspirate results were reviewed. The clinical data provided by clinicians were also noted. General Anesthesia was used in (439) patients, and local anesthesia was used in (321) patients. The procedure done under aseptic technique, aspiration sampling was generally performed before biopsy; the site of aspirate usually from the posterior iliac crest except for those less than 12 months where the tibia was the preferable site of aspiration Results: There were a total of 757 performed bone marrow aspirations. The main indications for bone marrow examination  were the following:256 (34%) for diagnosis and follow up of leukemia ,154 (20%)  for evaluation of fever of unknown origin,95 (13%)  for evaluation of  hepatosplenomegaly, lymphadenopathy and\or pallor, 54 (7%) for evaluation of solid tumors , 49 (6%) for evaluation of thrombocytopenia,48 (6%)  for evaluation of  pancytopenia,36 (5%) for evaluation of lymphoma, 29 (4%) for  suspected storage or metabolic diseases, 21(3%) for evaluation of undiagnosed masses in the abdomen, mediastinum, neck and jaw;12 (1.6%) for evaluation of unexplained  anemia,3 (0.4%) for others. The most common results reported were: 312 (65%) normal BMA, 71 (14.5%) acute leukemia, 17 (3%) marrow involvement by malignancy (solid tumors, Non –Hodgkin Lymphoma), 8 (2%) megaloblastic anemia, 8 (2%) erythropoietic hyperplasia, 8 (2%) proliferation of reactive histiocytes with activehemophagocytosis, 4 (1%) kala azar. Conclusions: The most common indication for this procedure in this hospital was to confirm diagnosis and follow up of acute leukemia.There is high rate of negative bone marrow examination which is unnecessarily done due to lack of further diagnostic facilities, also a high rate of non- informative results which might reflect inadequate experience of doctors performing the procedure. No complications were reported

Chronic immune thrombocytopenic purpura in children overview of 60 patients

Background: A small percentage of children with Immune thrombocytopenic purpura (ITP) suffer from a clinically significant disease with severe thrombocytopenia that requires intervention. Treatment for these children presents a challenge as there are few known therapies that offer long-term remission, and all that are known have significant side effects and toxicities. Aim of the study: To evaluate the effects of a variety of treatment modalities on the clinical course, and long treatment outcomes in children with chronic ITP. Patients & methods: A study involved 60 children with chronic ITP who were referred to Hemato-Oncology unit/Children's Welfare Teaching Hospital/Medical City/Baghdad. Treatment of patients included steroid, Intravenous Immunoglobulins, Anti D immunoglobulin, 6-Mercaptopurine, Rituximab and splenectomy. The Period of data collection and analysis was from May 2009 to May 2011. Results: The most common presenting symptom was skin bleeding, seen in 42 (70%) patients. Thirty-four patients received one or more courses of steroids. Complete response was achieved in 7 (20.5%) patients while there was no response in 12 (35.2%) patients, Intravenous immunoglobulin was used for 5 patients, only one (16%) exhibited a good response. Anti D Immunoglobulin was used in six patients; only one (8.3%) patient got good response. Twelve patients received 6-mercaptopurine, only one (8.3%) patient had a partial response. Six patients received Rituximab; three (50%) had a partial response. Six patients underwent splenectomy; response was noted in 5/6 (83.3%) patients. At the end of the study; complete response was seen in 13 (22.4%) patients, partial in 19 (31.6%), no response in 28 (46.7%) patients. Conclusions: Splenectomy is the most effective treatment modality when treating children with chronic ITP whose symptoms are severe

KIT gene deletion in a gastrointestinal stromal tumor of the small intestine.

[No abstract available

Gastric Perforation as a Primary Manifestation of Lymphomatoid Granulomatosis

[No abstract available

MECC Regional Initiative in Pediatric Palliative Care: Middle Eastern Course on Pain Management

In all the major medical centers throughout the Middle East, there is a functioning pediatric hematology oncology department. In almost all countries, opioids such as morphine, oxycodone, and fentanyl are available. Pediatric palliative care services are still in their infancy and await further recognition and development. Unfortunately, there are still countries in the Middle East where children with cancer are diagnosed when the disease is already at stage III or IV, when the only option left is palliation. To decrease the incidence of laic presentation, more effort is needed concerning public awareness, and concomitantly, an urgent need to develop hospital-based and community-based palliative and supportive care services. The initial step in this direction would involve more training of health care providers: Pediatricians, Pediatric Oncologists, Oncology Nurses, and Social Workers with updated pharmacological and nonpharmacological modalities of treatment

Treatment of Children With B-Cell Non-Hodgkin Lymphoma in a Low-Income Country

Background. An adapted LMB 96 derived protocol for B-cell non-Hodgkin lymphoma (NHL) was implemented at the pediatric oncology unit of the Children Welfare Teaching Hospital in Baghdad (Iraq) from 2000 to present. The purpose was to evaluate the feasibility and efficacy of this intensive therapeutic regimen in a limited resource country. Methods. Patients <15 years of age with high grade B-cell NHL were included. A modified LMB 96 regimen was employed with a reduction of cyclophosphamide and methotrexate dosages due to inadequate laboratory facilities and supportive care. Results. Between 2000 and 2005, 261 children with non-lymphoblastic NHL were registered; 239 were eligible for the analysis. Two patients had stage I disease, 20 stage II, 179 stage III, and 38 stage IV. Fifty-two patients (22%) had bulky disease. Twelve children were assigned to therapeutic group A (low risk),184 to group B (intermediate risk), and 43 to group C (high risk). One hundred, and eighty-four patients (77%) had a complete response after the COP pre-phase. Sixty-nine patients (29%) died during treatment. Twenty-nine patients abandoned treatment. At 24 months, the overall survival rate of the entire patient population was 66% (CI 95%: 62.2-70.6) and the event-free survival rate 53.3% (CI 95%: 50.0-56.8). Conclusions. The treatment schedule proved effective, but the treatment-related mortality due to infections and metabolic complications was very high owing to the limited supportive care available. The high rate of treatment abandonment was also an important cause of failure, especially for children living far away from the hospital. Blood Cancer 2011;56:560-567. (C) 2010 Wiley-Liss, Inc